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Yorodumi- PDB-3k2f: Nitric oxide-donating carbonic anhydrase inhibitors for the treat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k2f | ||||||
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Title | Nitric oxide-donating carbonic anhydrase inhibitors for the treatment of open-angle glaucoma | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / carbonic anhydrase / NO-donating agent / antiglaucoma drug / sulfonamide / Xray crystallography / Acetylation / Cytoplasm / Disease mutation / Metal-binding / Polymorphism / Zinc | ||||||
Function / homology | Function and homology information positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Temperini, C. / Cecchi, A. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: Nitric oxide-donating carbonic anhydrase inhibitors for the treatment of open-angle glaucoma Authors: Steele, R.M. / Benedini, F. / Biondi, S. / Borghi, V. / Carzaniga, L. / Impagnatiello, F. / Miglietta, D. / Chong, W.K. / Rajapakse, R. / Cecchi, A. / Temperini, C. / Supuran, C.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k2f.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k2f.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 3k2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/3k2f ftp://data.pdbj.org/pub/pdb/validation_reports/k2/3k2f | HTTPS FTP |
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-Related structure data
Related structure data | 1ca2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29289.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-HG / |
#4: Chemical | ChemComp-NKX / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: Tris.HCl pH7.7-7.8, sodium 4-(hydroxymercury)benzoate, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å |
Detector | Type: OXFORD SAPPHIRE CCD / Detector: CCD / Date: May 7, 2008 |
Radiation | Monochromator: capillary / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→69.1 Å / Num. obs: 16290 / Observed criterion σ(F): 2 / Redundancy: 3.3 % / Rsym value: 0.144 / Net I/σ(I): 4.44 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CA2 Resolution: 1.98→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.888 / SU B: 6.508 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.551 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.982→2.033 Å / Total num. of bins used: 20
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